ROSALIND Bioinformatics(16-20)

2019-04-14 20:22发布

站内文章 / 模拟电子
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刷题ROSALIND，练编程水平
http://rosalind.info/problems/list-view/

16. Finding a Protein Motif (寻找蛋白质模体)

6634703-7129eca0b43d61d7.png image.png
  • 解题思路
    • 为表示蛋白质模体的多种形式，设计以下表示形式：[XY]表示"既可以是X也可以是Y"，{X}表示"可以是除了X以外的任何一种氨基酸"。N-糖基化模体表示为 N{P}[ST]{P}
import urllib from urllib.request import urlopen import re list = ['A2Z669','B5ZC00','P07204_TRBM_HUMAN','P20840_SAG1_YEAST'] for name in list: # url地址拼接找蛋白质序列 url = 'http://www.uniprot.org/uniprot/'+name+'.fasta' # 获取url页面 req = urllib.request.Request(url) # 打开获取的 页面 response = urlopen(req) # 解读获取的页面 the_page = response.read() # 返回匹配到的' '的位置 start = the_page.find(b' M') # 把蛋白质序列拼接 seq = the_page[start+1:].replace(b' ',b'') seq = ' '+str(seq) # 正则表达式编译 regex = re.compile(r'N(?=[^P][ST][^P])') index = 0 out = [] while(index
  • 不了解urllib的看这里
把下面的数据粘贴到rosalind_mprt.txt，和python脚本放在一个文件夹下
>A2Z669 MRASRPVVHPVEAPPPAALAVAAAAVAVEAGVGAGGGAAAHGGENAQPRGVRMKDPPGAP GTPGGLGLRLVQAFFAAAALAVMASTDDFPSVSAFCYLVAAAILQCLWSLSLAVVDIYAL LVKRSLRNPQAVCIFTIGDGITGTLTLGAACASAGITVLIGNDLNICANNHCASFETATA MAFISWFALAPSCVLNFWSMASR >B5ZC00 MKNKFKTQEELVNHLKTVGFVFANSEIYNGLANAWDYGPLGVLLKNNLKNLWWKEFVTKQ KDVVGLDSAIILNPLVWKASGHLDNFSDPLIDCKNCKARYRADKLIESFDENIHIAENSS NEEFAKVLNDYEISCPTCKQFNWTEIRHFNLMFKTYQGVIEDAKNVVYLRPETAQGIFVN FKNVQRSMRLHLPFGIAQIGKSFRNEITPGNFIFRTREFEQMEIEFFLKEESAYDIFDKY LNQIENWLVSACGLSLNNLRKHEHPKEELSHYSKKTIDFEYNFLHGFSELYGIAYRTNYD LSVHMNLSKKDLTYFDEQTKEKYVPHVIEPSVGVERLLYAILTEATFIEKLENDDERILM DLKYDLAPYKIAVMPLVNKLKDKAEEIYGKILDLNISATFDNSGSIGKRYRRQDAIGTIY CLTIDFDSLDDQQDPSFTIRERNSMAQKRIKLSELPLYLNQKAHEDFQRQCQK >P07204_TRBM_HUMAN MLGVLVLGALALAGLGFPAPAEPQPGGSQCVEHDCFALYPGPATFLNASQICDGLRGHLM TVRSSVAADVISLLLNGDGGVGRRRLWIGLQLPPGCGDPKRLGPLRGFQWVTGDNNTSYS RWARLDLNGAPLCGPLCVAVSAAEATVPSEPIWEEQQCEVKADGFLCEFHFPATCRPLAV EPGAAAAAVSITYGTPFAARGADFQALPVGSSAAVAPLGLQLMCTAPPGAVQGHWAREAP GAWDCSVENGGCEHACNAIPGAPRCQCPAGAALQADGRSCTASATQSCNDLCEHFCVPNP DQPGSYSCMCETGYRLAADQHRCEDVDDCILEPSPCPQRCVNTQGGFECHCYPNYDLVDG ECVEPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQMFCNQTACPADCDPN TQASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALARHIGTDC DSGKVDGGDSGSGEPPPSPTPGSTLTPPAVGLVHSGLLIGISIASLCLVVALLALLCHLR KKQGAARAKMEYKCAAPSKEVVLQHVRTERTPQRL >P20840_SAG1_YEAST MFTFLKIILWLFSLALASAININDITFSNLEITPLTANKQPDQGWTATFDFSIADASSIR EGDEFTLSMPHVYRIKLLNSSQTATISLADGTEAFKCYVSQQAAYLYENTTFTCTAQNDL SSYNTIDGSITFSLNFSDGGSSYEYELENAKFFKSGPMLVKLGNQMSDVVNFDPAAFTEN VFHSGRSTGYGSFESYHLGMYCPNGYFLGGTEKIDYDSSNNNVDLDCSSVQVYSSNDFND WWFPQSYNDTNADVTCFGSNLWITLDEKLYDGEMLWVNALQSLPANVNTIDHALEFQYTC LDTIANTTYATQFSTTREFIVYQGRNLGTASAKSSFISTTTTDLTSINTSAYSTGSISTV ETGNRTTSEVISHVVTTSTKLSPTATTSLTIAQTSIYSTDSNITVGTDIHTTSEVISDVE TISRETASTVVAAPTSTTGWTGAMNTYISQFTSSSFATINSTPIISSSAVFETSDASIVN VHTENITNTAAVPSEEPTFVNATRNSLNSFCSSKQPSSPSSYTSSPLVSSLSVSKTLLST SFTPSVPTSNTYIKTKNTGYFEHTALTTSSVGLNSFSETAVSSQGTKIDTFLVSSLIAYP SSASGSQLSGIQQNFTSTSLMISTYEGKASIFFSAELGSIIFLLLSYLLF from collections import OrderedDict import re seqTest = OrderedDict() with open('rosalind_mprt.txt', 'rt') as f: for line in f: line = line.rstrip() if line.startswith('>'): seqName = line[1:] seqTest[seqName] = '' continue seqTest[seqName] += line.upper() for i,seq in seqTest.items(): #print (type(i)) # 正则表达式编译 regex = re.compile(r'N(?=[^P][ST][^P])') index = 0 out = [] while(index

17. Inferring mRNA from Protein(从蛋白质推断mRNA的种类)

6634703-ecc83eaf1a7496cd.png image.png
  • 解题思路
    • 由于密码子的简并性，例如编码丙氨酸（字符A）的密码子就有4种。
    • 现在给定一个蛋白字符串，要求其可能的编码RNA的种数。
translate_table={ "UUU":"F", "CUU":"L", "AUU":"I", "GUU":"V", "UUC":"F", "CUC":"L", "AUC":"I", "GUC":"V", "UUA":"L", "CUA":"L", "AUA":"I", "GUA":"V", "UUG":"L", "CUG":"L", "AUG":"M", "GUG":"V", "UCU":"S", "CCU":"P", "ACU":"T", "GCU":"A", "UCC":"S", "CCC":"P", "ACC":"T", "GCC":"A", "UCA":"S", "CCA":"P", "ACA":"T", "GCA":"A", "UCG":"S", "CCG":"P", "ACG":"T", "GCG":"A", "UAU":"Y", "CAU":"H", "AAU":"N", "GAU":"D", "UAC":"Y", "CAC":"H", "AAC":"N", "GAC":"D", "UAA":"*", "CAA":"Q", "AAA":"K", "GAA":"E", "UAG":"*", "CAG":"Q", "AAG":"K", "GAG":"E", "UGU":"C", "CGU":"R", "AGU":"S", "GGU":"G", "UGC":"C", "CGC":"R", "AGC":"S", "GGC":"G", "UGA":"*", "CGA":"R", "AGA":"R", "GGA":"G", "UGG":"W", "CGG":"R", "AGG":"R", "GGG":"G" } #改变密码子字典{'F': 2, 'L': 6, 'I': 3, 'V': 4, 'M': 1, 'S': 6, 'P': 4, 'T': 4, 'A': 4, 'Y': 2, 'H': 2, 'N': 2, 'D': 2, 'Q': 2, 'K': 2, 'E': 2, 'C': 2, 'R': 6, 'G': 4, 'W': 1} translate_count_table={} for aminoacid,pro in translate_table.items(): if pro =="*": pass elif pro not in translate_count_table.keys(): translate_count_table[pro] = 1 else: translate_count_table[pro] += 1 def modfind(protein): possiblerna = 1 for aminoacid in protein: possiblerna *= translate_count_table[aminoacid] return 3*possiblerna % 1000000 # Test print (modfind("MA")) 12

18. Open Reading Frames (开放阅读框)

6634703-92355a53fafa6d26.png image.png
  • 解题思路
    • 开放阅读框[open reading frame，ORF] 是结构基因的正常核苷酸序列，从起始密码子到终止密码子的阅读框可编码完整的多肽链，其间不存在使翻译中断的终止密码子。
    • 在mRNA序列中，每三个连续碱基(即三联“ 密码子”） 编码相应的氨基酸。其中有一个起始密码子AUG和三个终止密码子UAA，UAG，UGA。核糖体从起始密码子开始翻译，沿着mRNA序列合成多肽链并不断延伸，遇到终止密码子时，多肽链的延伸反应终止。由于读写位置不同，ORF在两条链上具有六种可能性。
def orf(sequence): # 读互补链 rev_seq = sequence[::-1].replace('C','g').replace('G','c').replace('T','a').replace('A','t').upper() codonTable = { 'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T', 'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K', 'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R', 'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q', 'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R', 'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A', 'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', 'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L', 'TAC':'Y', 'TAT':'Y', 'TAA':'', 'TAG':'', 'TGC':'C', 'TGT':'C', 'TGA':'', 'TGG':'W', } pro_list = [] for start in range(len(sequence)-3): proUeinsequence = '' # ATG 是启动子 if codonTable[sequence[start:start+3]] == 'M': # 开始遍历翻译 for n in range(start,len(sequence),3): if sequence[n:n+3] in codonTable.keys(): # 拼接出字符窜 proUeinsequence += codonTable[sequence[n:n+3]] # 遍历到最后为空 if codonTable[sequence[n:n+3]] == '': # 如果字符窜不为空 if proUeinsequence != '': # 把字符窜加入字典 pro_list.append(proUeinsequence) break # 遍历互补链 for start in range(len(rev_seq)-3): proUeinsequence = '' if codonTable[rev_seq[start:start+3]] == 'M': for n in range(start,len(rev_seq),3): if rev_seq[n:n+3] in codonTable.keys(): proUeinsequence += codonTable[rev_seq[n:n+3]] if codonTable[rev_seq[n:n+3]] == '': if proUeinsequence != '': pro_list.append(proUeinsequence) break # 返回找到启动子的正反链的集合 return set(pro_list) # 创建一个list， seq_list = [] stseq = '' for line in open('18_Open_reading_frames.txt'): if line[0] == '>': if stseq != '': seq_list.append(stseq) stseq = '' else: stseq = stseq + line.strip(' ') seq_list.append(stseq) proteins = orf(seq_list[0]) for one in proteins: print (one) M MLLGSFRLIPKETLIQVAGSSPCNLS MGMTPRLGLESLLE MTPRLGLESLLE 6634703-f0cd5292fe494e46.png image.png

19. Enumerating Gene Orders(穷举排列)

6634703-9d28054ea9337d94.png image.png
  • 解题思路
    • 给定n，要求给出所有排列。
    • 第一行给出排列数目，接下去输出所有排列组合
import itertools set1 = [] n = int(input("请输入一个整数：")) a = n*(n-1) print(a) for i in range(1,n+1): set1.append(i) b = itertools.permutations(set1,n) for one in list(b): print (' '.join(map(str,list(one)))) 6634703-d6f436680669784f.png image.png

20. Calculating Protein Mass(计算蛋白质质量)

6634703-d5dbf3a3e33728eb.png image.png
  • 解题思路
    • 参考蛋白质质量表
table = { 'A': 71.03711, 'C': 103.00919, 'D': 115.02694, 'E': 129.04259, 'F': 147.06841, 'G': 57.02146, 'H': 137.05891, 'I': 113.08406, 'K': 128.09496, 'L': 113.08406, 'M': 131.04049, 'N': 114.04293, 'P': 97.05276, 'Q': 128.05858, 'R': 156.10111, 'S': 87.03203, 'T': 101.04768, 'V': 99.06841, 'W': 186.07931, 'Y': 163.06333 } string ='SKADYEK' weight = 0 for i in string: if i in table.keys(): weight += table[i] print (weight) 821.3919199999999

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